Breast cancer is a heterogeneous disease associated with variable clinical outcomes despite standard local therapy for the primary tumor and systemic adjuvant therapy to prevent distant recurrence. Management decisions are typically made using classical prognostic and predictive clinicopathologic factors, and more recently gene expression profiling assays are commonly used in practice. Recent advances in genomic sequencing-often referred to collectively as next-generation sequencing (NGS)-have facilitated more in-depth evaluation of the cancer genome than could be afforded by the initial generation of gene expression studies, including DNA single nucleotide variants, small insertions and deletions, structural alterations, and copy number alterations (CNAs). In addition, this information has been integrated with other molecular profiling methods of processes that affect gene transcription (e.g., epigenetic, microRNA) and protein expression-the ultimate readout of the genetic code. Although NGS has provided new insights on the classification of breast cancer and identified potential predictive biomarkers and novel targets, there are formidable logistical and scientific obstacles that must be addressed before the promise of this technology is fully realized.